diff --git a/AnoPrimer/AnoPrimer.py b/AnoPrimer/AnoPrimer.py
index 6b85da3..1f76574 100644
--- a/AnoPrimer/AnoPrimer.py
+++ b/AnoPrimer/AnoPrimer.py
@@ -10,9 +10,6 @@
 from matplotlib import patches
 from plotly.subplots import make_subplots
 
-ag3 = malariagen_data.Ag3(url="gs://vo_agam_release/", pre=True)
-af1 = malariagen_data.Af1(url="gs://vo_afun_release/", pre=True)
-
 
 def retrieve_data_resource(species):
     assert species in [
@@ -20,9 +17,9 @@ def retrieve_data_resource(species):
         "funestus",
     ], f"species {species} not recognised, please use 'gambiae_sl' or 'funestus'"
     if species == "gambiae_sl":
-        data_resource = ag3
+        data_resource = malariagen_data.Ag3(url="gs://vo_agam_release/", pre=True)
     elif species == "funestus":
-        data_resource = af1
+        data_resource = malariagen_data.Af1(url="gs://vo_afun_release/", pre=True)
     return data_resource
 
 
@@ -605,7 +602,9 @@ def plot_primer_locs(
     # plot the legend
     plt.legend(handles=handles, loc=legend_loc)
     if out_dir:
-        fig.savefig(f"{out_dir}/{assay_name}_primer_locs.png", dpi=300)
+        fig.savefig(
+            f"{out_dir}/{assay_name}_primer_locs.png", dpi=300, bbox_inches="tight"
+        )
 
 
 def gget_blat_genome(primer_df, assay_type, assembly="anoGam3"):
@@ -1256,21 +1255,24 @@ def check_my_oligo(
     contig = contig.replace("chr", "")
     region_span = f"{contig}:{start}-{end}"
     print("plotting frequencies in ag3 data")
+
     fig = plot_sequence_frequencies(
+        data_resource=malariagen_data.Ag3(url="gs://vo_agam_release/", pre=True),
         region=region_span,
         sample_sets=sample_sets,
         sample_query=sample_query,
         width=width,
         height=height,
     )
+    return fig
 
 
 def plot_sequence_frequencies(
-    region, sample_sets=None, sample_query=None, width=700, height=400
+    data_resource, region, sample_sets=None, sample_query=None, width=700, height=400
 ):
     """Retrieve frequencies"""
 
-    snps = ag3.snp_calls(
+    snps = data_resource.snp_calls(
         region=region, sample_sets=sample_sets, sample_query=sample_query
     )
     ref_alt_arr = snps["variant_allele"].compute().values.astype(str)
diff --git a/docs/AnoPrimer-docs/_toc.yml b/docs/AnoPrimer-docs/_toc.yml
index 4e21f99..a363837 100644
--- a/docs/AnoPrimer-docs/_toc.yml
+++ b/docs/AnoPrimer-docs/_toc.yml
@@ -5,4 +5,5 @@ parts:
   chapters:
     - file: notebooks/api
     - file: notebooks/notebooks
+    - file: notebooks/data_access
     - file: notebooks/troubleshooting_contributing
diff --git a/notebooks/AnoPrimer-short.ipynb b/notebooks/AnoPrimer-short.ipynb
index 8473b12..dc84e5c 100644
--- a/notebooks/AnoPrimer-short.ipynb
+++ b/notebooks/AnoPrimer-short.ipynb
@@ -24,11 +24,592 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "id": "3md9Z9mRQRJn"
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/javascript": [
+       "(function(root) {\n",
+       "  function now() {\n",
+       "    return new Date();\n",
+       "  }\n",
+       "\n",
+       "  const force = true;\n",
+       "\n",
+       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
+       "    root._bokeh_onload_callbacks = [];\n",
+       "    root._bokeh_is_loading = undefined;\n",
+       "  }\n",
+       "\n",
+       "const JS_MIME_TYPE = 'application/javascript';\n",
+       "  const HTML_MIME_TYPE = 'text/html';\n",
+       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
+       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
+       "\n",
+       "  /**\n",
+       "   * Render data to the DOM node\n",
+       "   */\n",
+       "  function render(props, node) {\n",
+       "    const script = document.createElement(\"script\");\n",
+       "    node.appendChild(script);\n",
+       "  }\n",
+       "\n",
+       "  /**\n",
+       "   * Handle when an output is cleared or removed\n",
+       "   */\n",
+       "  function handleClearOutput(event, handle) {\n",
+       "    function drop(id) {\n",
+       "      const view = Bokeh.index.get_by_id(id)\n",
+       "      if (view != null) {\n",
+       "        view.model.document.clear()\n",
+       "        Bokeh.index.delete(view)\n",
+       "      }\n",
+       "    }\n",
+       "\n",
+       "    const cell = handle.cell;\n",
+       "\n",
+       "    const id = cell.output_area._bokeh_element_id;\n",
+       "    const server_id = cell.output_area._bokeh_server_id;\n",
+       "\n",
+       "    // Clean up Bokeh references\n",
+       "    if (id != null) {\n",
+       "      drop(id)\n",
+       "    }\n",
+       "\n",
+       "    if (server_id !== undefined) {\n",
+       "      // Clean up Bokeh references\n",
+       "      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
+       "      cell.notebook.kernel.execute(cmd_clean, {\n",
+       "        iopub: {\n",
+       "          output: function(msg) {\n",
+       "            const id = msg.content.text.trim()\n",
+       "            drop(id)\n",
+       "          }\n",
+       "        }\n",
+       "      });\n",
+       "      // Destroy server and session\n",
+       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
+       "      cell.notebook.kernel.execute(cmd_destroy);\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  /**\n",
+       "   * Handle when a new output is added\n",
+       "   */\n",
+       "  function handleAddOutput(event, handle) {\n",
+       "    const output_area = handle.output_area;\n",
+       "    const output = handle.output;\n",
+       "\n",
+       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
+       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
+       "      return\n",
+       "    }\n",
+       "\n",
+       "    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
+       "\n",
+       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
+       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
+       "      // store reference to embed id on output_area\n",
+       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
+       "    }\n",
+       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
+       "      const bk_div = document.createElement(\"div\");\n",
+       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
+       "      const script_attrs = bk_div.children[0].attributes;\n",
+       "      for (let i = 0; i < script_attrs.length; i++) {\n",
+       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
+       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
+       "      }\n",
+       "      // store reference to server id on output_area\n",
+       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  function register_renderer(events, OutputArea) {\n",
+       "\n",
+       "    function append_mime(data, metadata, element) {\n",
+       "      // create a DOM node to render to\n",
+       "      const toinsert = this.create_output_subarea(\n",
+       "        metadata,\n",
+       "        CLASS_NAME,\n",
+       "        EXEC_MIME_TYPE\n",
+       "      );\n",
+       "      this.keyboard_manager.register_events(toinsert);\n",
+       "      // Render to node\n",
+       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
+       "      render(props, toinsert[toinsert.length - 1]);\n",
+       "      element.append(toinsert);\n",
+       "      return toinsert\n",
+       "    }\n",
+       "\n",
+       "    /* Handle when an output is cleared or removed */\n",
+       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
+       "    events.on('delete.Cell', handleClearOutput);\n",
+       "\n",
+       "    /* Handle when a new output is added */\n",
+       "    events.on('output_added.OutputArea', handleAddOutput);\n",
+       "\n",
+       "    /**\n",
+       "     * Register the mime type and append_mime function with output_area\n",
+       "     */\n",
+       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
+       "      /* Is output safe? */\n",
+       "      safe: true,\n",
+       "      /* Index of renderer in `output_area.display_order` */\n",
+       "      index: 0\n",
+       "    });\n",
+       "  }\n",
+       "\n",
+       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
+       "  if (root.Jupyter !== undefined) {\n",
+       "    const events = require('base/js/events');\n",
+       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
+       "\n",
+       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
+       "      register_renderer(events, OutputArea);\n",
+       "    }\n",
+       "  }\n",
+       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
+       "    root._bokeh_timeout = Date.now() + 5000;\n",
+       "    root._bokeh_failed_load = false;\n",
+       "  }\n",
+       "\n",
+       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
+       "     \"<div style='background-color: #fdd'>\\n\"+\n",
+       "     \"<p>\\n\"+\n",
+       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
+       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
+       "     \"</p>\\n\"+\n",
+       "     \"<ul>\\n\"+\n",
+       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
+       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
+       "     \"</ul>\\n\"+\n",
+       "     \"<code>\\n\"+\n",
+       "     \"from bokeh.resources import INLINE\\n\"+\n",
+       "     \"output_notebook(resources=INLINE)\\n\"+\n",
+       "     \"</code>\\n\"+\n",
+       "     \"</div>\"}};\n",
+       "\n",
+       "  function display_loaded() {\n",
+       "    const el = document.getElementById(null);\n",
+       "    if (el != null) {\n",
+       "      el.textContent = \"BokehJS is loading...\";\n",
+       "    }\n",
+       "    if (root.Bokeh !== undefined) {\n",
+       "      if (el != null) {\n",
+       "        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n",
+       "      }\n",
+       "    } else if (Date.now() < root._bokeh_timeout) {\n",
+       "      setTimeout(display_loaded, 100)\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  function run_callbacks() {\n",
+       "    try {\n",
+       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
+       "        if (callback != null)\n",
+       "          callback();\n",
+       "      });\n",
+       "    } finally {\n",
+       "      delete root._bokeh_onload_callbacks\n",
+       "    }\n",
+       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
+       "  }\n",
+       "\n",
+       "  function load_libs(css_urls, js_urls, callback) {\n",
+       "    if (css_urls == null) css_urls = [];\n",
+       "    if (js_urls == null) js_urls = [];\n",
+       "\n",
+       "    root._bokeh_onload_callbacks.push(callback);\n",
+       "    if (root._bokeh_is_loading > 0) {\n",
+       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
+       "      return null;\n",
+       "    }\n",
+       "    if (js_urls == null || js_urls.length === 0) {\n",
+       "      run_callbacks();\n",
+       "      return null;\n",
+       "    }\n",
+       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
+       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
+       "\n",
+       "    function on_load() {\n",
+       "      root._bokeh_is_loading--;\n",
+       "      if (root._bokeh_is_loading === 0) {\n",
+       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
+       "        run_callbacks()\n",
+       "      }\n",
+       "    }\n",
+       "\n",
+       "    function on_error(url) {\n",
+       "      console.error(\"failed to load \" + url);\n",
+       "    }\n",
+       "\n",
+       "    for (let i = 0; i < css_urls.length; i++) {\n",
+       "      const url = css_urls[i];\n",
+       "      const element = document.createElement(\"link\");\n",
+       "      element.onload = on_load;\n",
+       "      element.onerror = on_error.bind(null, url);\n",
+       "      element.rel = \"stylesheet\";\n",
+       "      element.type = \"text/css\";\n",
+       "      element.href = url;\n",
+       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
+       "      document.body.appendChild(element);\n",
+       "    }\n",
+       "\n",
+       "    for (let i = 0; i < js_urls.length; i++) {\n",
+       "      const url = js_urls[i];\n",
+       "      const element = document.createElement('script');\n",
+       "      element.onload = on_load;\n",
+       "      element.onerror = on_error.bind(null, url);\n",
+       "      element.async = false;\n",
+       "      element.src = url;\n",
+       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
+       "      document.head.appendChild(element);\n",
+       "    }\n",
+       "  };\n",
+       "\n",
+       "  function inject_raw_css(css) {\n",
+       "    const element = document.createElement(\"style\");\n",
+       "    element.appendChild(document.createTextNode(css));\n",
+       "    document.body.appendChild(element);\n",
+       "  }\n",
+       "\n",
+       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.3.4.min.js\"];\n",
+       "  const css_urls = [];\n",
+       "\n",
+       "  const inline_js = [    function(Bokeh) {\n",
+       "      Bokeh.set_log_level(\"info\");\n",
+       "    },\n",
+       "function(Bokeh) {\n",
+       "    }\n",
+       "  ];\n",
+       "\n",
+       "  function run_inline_js() {\n",
+       "    if (root.Bokeh !== undefined || force === true) {\n",
+       "          for (let i = 0; i < inline_js.length; i++) {\n",
+       "      inline_js[i].call(root, root.Bokeh);\n",
+       "    }\n",
+       "} else if (Date.now() < root._bokeh_timeout) {\n",
+       "      setTimeout(run_inline_js, 100);\n",
+       "    } else if (!root._bokeh_failed_load) {\n",
+       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
+       "      root._bokeh_failed_load = true;\n",
+       "    } else if (force !== true) {\n",
+       "      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n",
+       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  if (root._bokeh_is_loading === 0) {\n",
+       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
+       "    run_inline_js();\n",
+       "  } else {\n",
+       "    load_libs(css_urls, js_urls, function() {\n",
+       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
+       "      run_inline_js();\n",
+       "    });\n",
+       "  }\n",
+       "}(window));"
+      ],
+      "application/vnd.bokehjs_load.v0+json": "(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    const el = document.getElementById(null);\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.3.4.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n          for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/javascript": [
+       "(function(root) {\n",
+       "  function now() {\n",
+       "    return new Date();\n",
+       "  }\n",
+       "\n",
+       "  const force = true;\n",
+       "\n",
+       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
+       "    root._bokeh_onload_callbacks = [];\n",
+       "    root._bokeh_is_loading = undefined;\n",
+       "  }\n",
+       "\n",
+       "const JS_MIME_TYPE = 'application/javascript';\n",
+       "  const HTML_MIME_TYPE = 'text/html';\n",
+       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
+       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
+       "\n",
+       "  /**\n",
+       "   * Render data to the DOM node\n",
+       "   */\n",
+       "  function render(props, node) {\n",
+       "    const script = document.createElement(\"script\");\n",
+       "    node.appendChild(script);\n",
+       "  }\n",
+       "\n",
+       "  /**\n",
+       "   * Handle when an output is cleared or removed\n",
+       "   */\n",
+       "  function handleClearOutput(event, handle) {\n",
+       "    function drop(id) {\n",
+       "      const view = Bokeh.index.get_by_id(id)\n",
+       "      if (view != null) {\n",
+       "        view.model.document.clear()\n",
+       "        Bokeh.index.delete(view)\n",
+       "      }\n",
+       "    }\n",
+       "\n",
+       "    const cell = handle.cell;\n",
+       "\n",
+       "    const id = cell.output_area._bokeh_element_id;\n",
+       "    const server_id = cell.output_area._bokeh_server_id;\n",
+       "\n",
+       "    // Clean up Bokeh references\n",
+       "    if (id != null) {\n",
+       "      drop(id)\n",
+       "    }\n",
+       "\n",
+       "    if (server_id !== undefined) {\n",
+       "      // Clean up Bokeh references\n",
+       "      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
+       "      cell.notebook.kernel.execute(cmd_clean, {\n",
+       "        iopub: {\n",
+       "          output: function(msg) {\n",
+       "            const id = msg.content.text.trim()\n",
+       "            drop(id)\n",
+       "          }\n",
+       "        }\n",
+       "      });\n",
+       "      // Destroy server and session\n",
+       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
+       "      cell.notebook.kernel.execute(cmd_destroy);\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  /**\n",
+       "   * Handle when a new output is added\n",
+       "   */\n",
+       "  function handleAddOutput(event, handle) {\n",
+       "    const output_area = handle.output_area;\n",
+       "    const output = handle.output;\n",
+       "\n",
+       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
+       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
+       "      return\n",
+       "    }\n",
+       "\n",
+       "    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
+       "\n",
+       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
+       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
+       "      // store reference to embed id on output_area\n",
+       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
+       "    }\n",
+       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
+       "      const bk_div = document.createElement(\"div\");\n",
+       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
+       "      const script_attrs = bk_div.children[0].attributes;\n",
+       "      for (let i = 0; i < script_attrs.length; i++) {\n",
+       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
+       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
+       "      }\n",
+       "      // store reference to server id on output_area\n",
+       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  function register_renderer(events, OutputArea) {\n",
+       "\n",
+       "    function append_mime(data, metadata, element) {\n",
+       "      // create a DOM node to render to\n",
+       "      const toinsert = this.create_output_subarea(\n",
+       "        metadata,\n",
+       "        CLASS_NAME,\n",
+       "        EXEC_MIME_TYPE\n",
+       "      );\n",
+       "      this.keyboard_manager.register_events(toinsert);\n",
+       "      // Render to node\n",
+       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
+       "      render(props, toinsert[toinsert.length - 1]);\n",
+       "      element.append(toinsert);\n",
+       "      return toinsert\n",
+       "    }\n",
+       "\n",
+       "    /* Handle when an output is cleared or removed */\n",
+       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
+       "    events.on('delete.Cell', handleClearOutput);\n",
+       "\n",
+       "    /* Handle when a new output is added */\n",
+       "    events.on('output_added.OutputArea', handleAddOutput);\n",
+       "\n",
+       "    /**\n",
+       "     * Register the mime type and append_mime function with output_area\n",
+       "     */\n",
+       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
+       "      /* Is output safe? */\n",
+       "      safe: true,\n",
+       "      /* Index of renderer in `output_area.display_order` */\n",
+       "      index: 0\n",
+       "    });\n",
+       "  }\n",
+       "\n",
+       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
+       "  if (root.Jupyter !== undefined) {\n",
+       "    const events = require('base/js/events');\n",
+       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
+       "\n",
+       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
+       "      register_renderer(events, OutputArea);\n",
+       "    }\n",
+       "  }\n",
+       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
+       "    root._bokeh_timeout = Date.now() + 5000;\n",
+       "    root._bokeh_failed_load = false;\n",
+       "  }\n",
+       "\n",
+       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
+       "     \"<div style='background-color: #fdd'>\\n\"+\n",
+       "     \"<p>\\n\"+\n",
+       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
+       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
+       "     \"</p>\\n\"+\n",
+       "     \"<ul>\\n\"+\n",
+       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
+       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
+       "     \"</ul>\\n\"+\n",
+       "     \"<code>\\n\"+\n",
+       "     \"from bokeh.resources import INLINE\\n\"+\n",
+       "     \"output_notebook(resources=INLINE)\\n\"+\n",
+       "     \"</code>\\n\"+\n",
+       "     \"</div>\"}};\n",
+       "\n",
+       "  function display_loaded() {\n",
+       "    const el = document.getElementById(null);\n",
+       "    if (el != null) {\n",
+       "      el.textContent = \"BokehJS is loading...\";\n",
+       "    }\n",
+       "    if (root.Bokeh !== undefined) {\n",
+       "      if (el != null) {\n",
+       "        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n",
+       "      }\n",
+       "    } else if (Date.now() < root._bokeh_timeout) {\n",
+       "      setTimeout(display_loaded, 100)\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  function run_callbacks() {\n",
+       "    try {\n",
+       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
+       "        if (callback != null)\n",
+       "          callback();\n",
+       "      });\n",
+       "    } finally {\n",
+       "      delete root._bokeh_onload_callbacks\n",
+       "    }\n",
+       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
+       "  }\n",
+       "\n",
+       "  function load_libs(css_urls, js_urls, callback) {\n",
+       "    if (css_urls == null) css_urls = [];\n",
+       "    if (js_urls == null) js_urls = [];\n",
+       "\n",
+       "    root._bokeh_onload_callbacks.push(callback);\n",
+       "    if (root._bokeh_is_loading > 0) {\n",
+       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
+       "      return null;\n",
+       "    }\n",
+       "    if (js_urls == null || js_urls.length === 0) {\n",
+       "      run_callbacks();\n",
+       "      return null;\n",
+       "    }\n",
+       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
+       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
+       "\n",
+       "    function on_load() {\n",
+       "      root._bokeh_is_loading--;\n",
+       "      if (root._bokeh_is_loading === 0) {\n",
+       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
+       "        run_callbacks()\n",
+       "      }\n",
+       "    }\n",
+       "\n",
+       "    function on_error(url) {\n",
+       "      console.error(\"failed to load \" + url);\n",
+       "    }\n",
+       "\n",
+       "    for (let i = 0; i < css_urls.length; i++) {\n",
+       "      const url = css_urls[i];\n",
+       "      const element = document.createElement(\"link\");\n",
+       "      element.onload = on_load;\n",
+       "      element.onerror = on_error.bind(null, url);\n",
+       "      element.rel = \"stylesheet\";\n",
+       "      element.type = \"text/css\";\n",
+       "      element.href = url;\n",
+       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
+       "      document.body.appendChild(element);\n",
+       "    }\n",
+       "\n",
+       "    for (let i = 0; i < js_urls.length; i++) {\n",
+       "      const url = js_urls[i];\n",
+       "      const element = document.createElement('script');\n",
+       "      element.onload = on_load;\n",
+       "      element.onerror = on_error.bind(null, url);\n",
+       "      element.async = false;\n",
+       "      element.src = url;\n",
+       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
+       "      document.head.appendChild(element);\n",
+       "    }\n",
+       "  };\n",
+       "\n",
+       "  function inject_raw_css(css) {\n",
+       "    const element = document.createElement(\"style\");\n",
+       "    element.appendChild(document.createTextNode(css));\n",
+       "    document.body.appendChild(element);\n",
+       "  }\n",
+       "\n",
+       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.3.4.min.js\"];\n",
+       "  const css_urls = [];\n",
+       "\n",
+       "  const inline_js = [    function(Bokeh) {\n",
+       "      Bokeh.set_log_level(\"info\");\n",
+       "    },\n",
+       "function(Bokeh) {\n",
+       "    }\n",
+       "  ];\n",
+       "\n",
+       "  function run_inline_js() {\n",
+       "    if (root.Bokeh !== undefined || force === true) {\n",
+       "          for (let i = 0; i < inline_js.length; i++) {\n",
+       "      inline_js[i].call(root, root.Bokeh);\n",
+       "    }\n",
+       "} else if (Date.now() < root._bokeh_timeout) {\n",
+       "      setTimeout(run_inline_js, 100);\n",
+       "    } else if (!root._bokeh_failed_load) {\n",
+       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
+       "      root._bokeh_failed_load = true;\n",
+       "    } else if (force !== true) {\n",
+       "      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n",
+       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  if (root._bokeh_is_loading === 0) {\n",
+       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
+       "    run_inline_js();\n",
+       "  } else {\n",
+       "    load_libs(css_urls, js_urls, function() {\n",
+       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
+       "      run_inline_js();\n",
+       "    });\n",
+       "  }\n",
+       "}(window));"
+      ],
+      "application/vnd.bokehjs_load.v0+json": "(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    const el = document.getElementById(null);\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.3.4.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n          for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "import AnoPrimer\n",
     "import pandas as pd"
@@ -49,7 +630,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {
     "id": "NCEovYA6RrH4"
    },
@@ -89,21 +670,31 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "id": "dfOtlN0IQb4p",
-    "scrolled": false
+    "id": "dfOtlN0IQb4p"
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Our genome sequence for 2L is 49364325 bp long\n",
+      "Exon junctions for AGAP006222-RA: [ 238  325  911 1353] [28524463, 28524621, 28525282, 28525790] \n",
+      "\n",
+      "Access SNP calls: ⠸ (0:00:03.53) "
+     ]
+    }
+   ],
    "source": [
     "primer_df, blat_df = AnoPrimer.designPrimers(\n",
-    "                                species='funestus',\n",
-    "                                assay_type='gDNA primers + probe',  # assay_type options are: 'cDNA primers', 'gDNA primers', 'gDNA primers + probe', 'probe'\n",
-    "                                target='2RL:22422652',                               #'AGAP000818-RA' target should be an AGAP/AFUN transcript identifier for qPCR, otherwise should be a contig:integer string in genome, such as '2L:28545767'\n",
-    "                                assay_name='funestus_random',\n",
+    "                                species='gambiae_sl',\n",
+    "                                assay_type='cDNA primers',  # assay_type options are: 'cDNA primers', 'gDNA primers', 'gDNA primers + probe', 'probe'\n",
+    "                                target='AGAP006222-RA',                               #'AGAP000818-RA' target should be an AGAP/AFUN transcript identifier for qPCR, otherwise should be a contig:integer string in genome, such as '2L:28545767'\n",
+    "                                assay_name='UGT222',\n",
     "                                n_primer_pairs=5,\n",
     "                                min_amplicon_size=60,\n",
     "                                max_amplicon_size=120,\n",
     "                                primer_parameters=\"default\",\n",
-    "                           #     sample_sets=['AG1000G-BF-A', 'AG1000G-GH', 'AG1000G-GN-A'],\n",
+    "                                sample_sets=['AG1000G-BF-A', 'AG1000G-GH', 'AG1000G-GN-A'],\n",
     "                                out_dir=\".\"\n",
     "                                )"
    ]
@@ -113,7 +704,9 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "primer_df"
+   ]
   }
  ],
  "metadata": {
@@ -136,9 +729,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.13"
+   "version": "3.11.0"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }